US20160223526A1 - Method of screening for compounds useful in the treatment of huntington disease - Google Patents

Method of screening for compounds useful in the treatment of huntington disease Download PDF

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US20160223526A1
US20160223526A1 US15/021,975 US201415021975A US2016223526A1 US 20160223526 A1 US20160223526 A1 US 20160223526A1 US 201415021975 A US201415021975 A US 201415021975A US 2016223526 A1 US2016223526 A1 US 2016223526A1
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mitochondria
area
average
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Nathalie Compagnone
Clotilde Biscarrat
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INNOVATIVE CONCEPTS IN DRUG DEVELOPMENT
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6893—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids related to diseases not provided for elsewhere
    • G01N33/6896—Neurological disorders, e.g. Alzheimer's disease
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/5076—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics involving cell organelles, e.g. Golgi complex, endoplasmic reticulum
    • G01N33/5079—Mitochondria
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/502—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5091—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing the pathological state of an organism
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/28—Neurological disorders
    • G01N2800/2835—Movement disorders, e.g. Parkinson, Huntington, Tourette
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Definitions

  • the present invention relates to the field of medicine, in particular to the diagnosis and treatment of Huntington disease.
  • Huntington disease is a progressive neurological disorder that leads to a distinctive chorea, cognitive loss, various psychological disorders, and eventually death.
  • HD is caused by the expansion of an unstable polymorphic trinucleotide (CAG)n repeat in exon 1 of the huntingtin (Htt) gene, which translates into an extended polyglutamine tract in the protein.
  • CAG polymorphic trinucleotide
  • Htt huntingtin
  • the Htt gene is a ubiquitous gene modulating several key functions in cells including transport, calcium homeostasis, neurotransmitter release, gene transcription, proteasome and mitochondrial function. From these complex molecular interactions derives a wide range of clinical patterns in the pathological progression of the disease.
  • HD diagnosis relies mostly on genetic testing, few studies exist to identify protein or imaging markers capable of identifying early progression signs of the disease in HD pre-symptomatic patients.
  • compounds capable of binding to TSPO have been postulated to be imaging markers for neurodegenerative diseases associated to inflammation including HD (e.g. the international patent application WO 10/020000; Politis et al., 2011).
  • TSPO peripheral benzodiazepine receptor
  • HD patients show depression, bradykinesia, cognitive impairment, aggressive behavior and other complications such as eating disorders.
  • the inventors Using molecular imaging of mitochondria in human live cells, the inventors identified a set of markers that is specific to HD and can be used to diagnose HD at early or asymptomatic stage of the disease. Furthermore, they demonstrated that the signature obtained with these markers can be reversed by treatments and thus provides a human-derived model to screen drugs capable of reversing disease progression of HD.
  • the present invention relates to a method, preferably an in vitro method, of screening for compounds useful in the treatment of Huntington disease, wherein the method comprises
  • the method may further comprise comparing the values obtained in step b) with the values obtained in absence of the test compound.
  • score (NC ⁇ Var)*100/(NC ⁇ PC)
  • NC is the value or average value obtained with HD sample(s) in absence of the test compound
  • PC is the value or average value obtained with healthy sample(s)
  • Var is the measured value of the variable.
  • a test compound may be identified as useful in the treatment of Huntington disease when all measured variables have a positive score.
  • the present invention also relates to a method, preferably an in vitro method, for diagnosing Huntington disease in a subject, wherein the method comprises:
  • the method may further comprise determining if said subject is affected with HD based on the measured values of mitochondrial behaviour variables.
  • the subject comprises 36 to 39 CAG repeats in the htt gene.
  • the method may further comprise calculating the z-scores of measured variables.
  • positive z-scores of the 1 st preferably V1, 2 nd and 4 th variables and negative z-scores of the 3 rd , 5 th , 6 th , preferably V29, and 7 th , preferably V32, variables are indicative that the subject suffers from Huntington disease.
  • the present invention further relates to a method, preferably an in vitro method, for monitoring the response of a subject affected with Huntington disease to therapy, wherein the method comprises
  • step b) comparing the measured values obtained in step a) for samples obtained before and after the administration of the treatment.
  • the patient is responsive to the therapy or is susceptible to benefit from the therapy when all measured variables have a positive score.
  • these methods may comprise measuring the mitochondrial behaviour variables V1, V12, V13, V15, V29 and V32, preferably V1, V12, V13, V15, V23, V29 and V32. They may also further comprises measuring at least one additional mitochondrial behaviour variable selected from the group consisting of V7, V30 V33 and V34.
  • These methods may further comprise comparing the measured values of mitochondrial behaviour variables with the values of said variables measured in a sample obtained from a healthy subject.
  • the sample is selected from the group consisting of skin biopsy sample, nervous tissue biopsy sample and serum or blood sample. More preferably, the sample is skin biopsy sample.
  • the cells may be selected from the group consisting of fibroblasts, induced pluripotent stem cells derived from fibroblasts, lymphocytes and neuronal cells.
  • the cells are fibroblasts.
  • the dispersion descriptor is selected from the group consisting of the variance, the standard deviation and an interquantile range, preferably the interquartile range.
  • mitochondria contained in said living cells are labelled.
  • Mitochondria may be labelled using any suitable label, preferably using a fluorescent label, and more preferably using MitoTracker Green.
  • the values of mitochondrial behaviour variables may be obtained from images captured using a fluorescence microscope or a differential interference-contrast (DIC) microscope coupled to a suitable image acquisition device, preferably a CCD camera.
  • DIC differential interference-contrast
  • the values of variables are obtained from images captured using a fluorescence microscope coupled to a CCD camera.
  • FIG. 1 Dendogram of the hierarchical cluster analysis applying the Ward's method.
  • FIG. 2 Heat map representation of the classification of the different subjects in the two subgroups identified by hierarchical clustering. The graph shows the z-scores values for the seven variables constituting the HD-signature.
  • FIG. 3 HD-signature of the invention shown by the z-score of each variable in healthy and diseased subject groups.
  • FIG. 4 Dose-response analysis of Resveratrol of the 7 different variables (V1, V32, V12, V13, V15, V23 and V29) of the HD-signature of the invention (% of phenotypic rescue).
  • FIG. 5 Weighted representation of the dose-response effect of Resveratrol on disease-modification.
  • FIG. 6 Dose-response analysis of Cyclosporine A on the 7 different variables (V1, V32, V12, V13, V15, V23 and V29) of the HD-signature of the invention (% of phenotypic rescue).
  • FIG. 7 Weighted representation of the dose-response effect of Cyclosporine A on disease-modification.
  • FIG. 8 Disease progression and schematic representation of the complexity of the different functional interactions resulting form the mutation of the single gene Htt.
  • This general strategy was disclosed in the U.S. Pat. No. 8,497,089, the content of which is herein enclosed in its entirety by reference. The inventors thus herein consider the global functionalities of the organelle and not solely the individual functions in cellular metabolism.
  • mitochondria are sensitive to the cellular environment and constantly communicate with this environment, they generate thousands of protein-protein interactions within the mitochondria and with other cellular organelles and compartments.
  • the inventors Using molecular imaging of mitochondria in live cells, the inventors experimentally and dynamically assessed the mitochondrial reticular system in live cells allowing the capture of the resultant of those interactions that describe the mitochondrial behaviour. They measured 37 mitochondrial behaviour variables relating to the motility, the morphology, the network organization and the permeability of the mitochondria.
  • Motility variables comprise, for example, measures of speed of displacement, amplitude, frequency and regularity of movements as well as distance traveled.
  • Morphology variables comprise, for example, measures of mitochondrial dynamics (fusion-fission balance) and the frequency of apparition of various typical morphological features.
  • the mitochondrial reticular network organization is scored with respect to its orientation, distribution and regionalization with respect to the intracellular cytoskeleton and/or to particular hot-spots in the cells such as the microtubule organizing center and focal adhesion points. Mitochondrial membrane permeability is measured by the dynamic analysis of signal intensity within individual mitochondria.
  • HD-signature comprising only seven mitochondrial behaviour variables that are sufficient to segregate healthy and HD patients. They further demonstrated that this signature can be pharmacologically reversed and can thus be used to screen compounds useful in the treatment of HD.
  • Huntington disease refers to an autosomal dominant progressive neurodegenerative disorder caused by an expanded trinucleotide repeat (CAG)n, encoding glutamine, in the gene encoding huntingtin (Gene ID: 3064) on chromosome 4p16.3.
  • CAG trinucleotide repeat
  • the number of repeats is from 6 to 35. Individuals with repeat number between 36 and 39 may develop HD and individuals with repeat number of 40 and above will develop HD.
  • the term “subject” or “patient” refers to an animal, preferably to a mammal, even more preferably to a human, including adult, child and human at the prenatal stage.
  • HD patient or “HD subject” refers to a subject having at least 36 CAG repeats in the Htt gene and who have developed or will develop HD.
  • the subject may be at asymptomatic or symptomatic stage of the disease.
  • the term “healthy patient” or “healthy subject” refers to a subject who is not affected with HD, in particular a subject having from 6 to 35 CAG repeats in the Htt gene. Preferably, the subject is not affected with any known disease, i.e. apparently healthy.
  • treatment refers to any act intended to ameliorate the health status of patients such as therapy, prevention and retardation of HD.
  • such term refers to the amelioration or eradication of HD or symptoms associated with HD, in particular neurological symptoms.
  • this term refers to minimizing the spread or worsening of HD resulting from the administration of one or more therapeutic agents to a subject affected with HD.
  • sample means any sample containing living cells derived from a subject.
  • samples include fluids such as blood, plasma, saliva, urine and seminal fluid samples as well as biopsies, organs, tissues or cell samples.
  • the sample is selected from the group consisting of skin biopsy, nervous tissue biopsy, serum and blood. More preferably, the sample is a skin biopsy.
  • the sample may be treated prior to its use.
  • skin biopsies may be treated to isolate fibroblasts cells. Fibroblasts may be isolated using any method known by the skilled person. For example, the dermal component of the skin may be cut into small pieces and treated over night with collagenase type 1 and dispase.
  • cells may be seeded in culture flasks and cultured in fibroblasts proliferation medium containing, for example, Dulbecco's minimum essential medium, 10% fetal calf serum, penicillin and streptomycin.
  • the term “dispersion descriptor” refers to a measure of dispersion denoted how stretched or squeezed is a distribution of values.
  • this descriptor is selected from the group consisting of the variance, the standard deviation, and an interquantile range.
  • the interquantile range is the interquartile range or the interdecile range.
  • the interquartile range is the difference between the upper and lower quartiles, i.e. between the 25 th percentile (splits lowest 25% of data) and the 75 th percentile (splits highest 25% of data).
  • the interdecile range is the difference between the 1 st and the 9 th deciles, i.e.
  • the dispersion descriptor is selected from the group consisting of the variance, the standard deviation and the interquartile range. Methods for calculating these values are commonly known by the skilled person.
  • the methods of the invention as disclosed below may be in vivo, ex vivo or in vitro methods, preferably in vitro methods.
  • the present invention concerns a method of screening for compounds useful in the treatment of HD, wherein the method comprises
  • V1 the average frequency of stops during trajectories of individual mitochondria
  • V34 the average frequency of burst during displacement of individual mitochondria, and a combination thereof
  • V12 the average number of individual mitochondria per unit of cell area, or a dispersion descriptor of the numbers of individual mitochondria per unit of cell area;
  • V13 the average area of mitochondria, or a dispersion descriptor of the areas of mitochondria
  • V15 the frequency of mitochondria displaying an area between 0.51 and 1 ⁇ m 2 ;
  • V29 the frequency of mitochondria displaying an area between 70 and 100 ⁇ m 2
  • V7 the total area of regions containing entwined mitochondria to the total cell area
  • V30 the frequency of mitochondria displaying an area between 100 and 200 ⁇ m 2 , and any combination thereof
  • V32 the average moving speed of mitochondria, or a dispersion descriptor of the moving speeds of mitochondria
  • V33 the average maximal moving speed of individual mitochondria, or a dispersion descriptor of maximal moving speeds of individual mitochondria, and a combination thereof.
  • the method further comprises providing a sample from a subject affected with HD.
  • the subject affected with HD may be at any stage of the disease, in particular in the asymptomatic stage or at early stage of the disease progression.
  • the subject comprises a mutation of the htt gene with at least 40 CAG repeats.
  • the screening method may be conducted on the sample of a HD patient in order to select a suitable therapy, i.e. personalized medicine, or on a population of HD samples, e.g. for drug development or drug repositioning.
  • a suitable therapy i.e. personalized medicine
  • a population of HD samples e.g. for drug development or drug repositioning.
  • the sample is selected from the group consisting of skin biopsy, nervous tissue biopsy, serum and blood.
  • living cells may be selected from the group consisting of fibroblasts, lymphocytes and neuronal cells directly obtained from the sample or from primary cultures of cells from said sample.
  • Living cells may also be induced pluripotent stem cells derived from adult somatic cells, in particular from fibroblasts obtained from the sample.
  • cells are non-transformed living cells to obtain results as close as possible of the in vivo situation.
  • the sample is a skin biopsy and cells are fibroblasts.
  • the skin biopsy may be treated in order to isolate or enriched the culture in fibroblasts.
  • the method further comprises, before measuring the values of mitochondrial behaviour variables, labelling mitochondria contained in living cells obtained from the sample.
  • mitochondria are labelled before step a).
  • Mitochondria may be labeled using any method commonly known by the skilled person.
  • the label is a fluorescent, luminescent or colored label. More preferably, the label is a fluorescent label.
  • Mitochondria may be labelled using a probe specific of said organelle and/or by transfection of a reporter gene (e.g. a GFP-expressing construct with mitochondrion-targeted expression) and/or by microinjection inside live cells of a marker or dye specifically taken up by said organelle. All these techniques are well known by the man skilled in the art and some commercial kits are available for this type of labelling and should be used according to manufacturer's recommendations.
  • mitochondria may be labelled using calcein and cobalt (Petronilli et al., 1998), fluorescent rhodamine derivatives such as Rhodamine 123, tetramethylrhodamine methyl ester (TMRM) and tetramethylrhodamine ethyl ester (TMRE), carbocyanine dyes, 10-N-Nonyl acridine orange (NAO) or a MitoTracker dye, in particular MitoTracker Green (MTG) or MitoTracker red (CMXRos).
  • TMRM tetramethylrhodamine methyl ester
  • TMRE tetramethylrhodamine ethyl ester
  • carbocyanine dyes 10-N-Nonyl acridine orange (NAO) or a MitoTracker dye, in particular MitoTracker Green (MTG) or MitoTracker red (CMXRos).
  • MMG MitoTracker Green
  • the dye can be selected from the group consisting of MitoTracker Green (MTG), carbocyanine dyes, 10-N-Nonyl acridine orange (NAO) and the combination calcein-cobalt.
  • MMG MitoTracker Green
  • carbocyanine dyes carbocyanine dyes
  • NAO 10-N-Nonyl acridine orange
  • mitochondria are labelled using MitoTracker Green.
  • mitochondria are not labelled and the values of the mitochondrial behaviour variables are measured using a label-free microscopic technique such as differential interference contrast (DIC) microscopy.
  • DIC differential interference contrast
  • step a) living cells are contacted with a test compound.
  • the test compound may be selected from the group consisting of chemical compounds, biological compounds, radiations, and any combination thereof.
  • the test compound is a radiation, in particular a radiation selected from the group consisting of X-rays, gamma rays, alpha particles, beta particles, photons, electrons, neutrons, radioisotopes, and other forms of ionizing radiation, and any combination thereof.
  • the test compound is a chemical compound, i.e. an organic or inorganic compound.
  • the test compound may be a drug authorized to be marketed for another application than HD, a compound from a high-throughput chemical library or a nucleic acid construct suitable for gene therapy. If the test compound is a drug authorized to be marketed for another application than HD, the method may be used for drug repositioning.
  • the test compound is a biological compound.
  • the biological compound may be selected from the group consisting of proteins, lipids, nucleic acids, carbohydrates and any other biological molecules or complexes. It may also be a therapeutic cell used for cell therapy or engineered virus for virotherapy.
  • therapeutic cells may be stem cells, progenitor cells, mature and functional cells for cell replacement therapy or genetically modified cells for cell-based gene therapy.
  • the technique for contacting living cells with the test compound may vary according to the nature of said compound and may be easily chosen by the skilled person.
  • the test compound is a chemical or biological compound, it may be added to the cell culture medium.
  • living cells obtained from the sample and therapeutic or genetically modified cells may be contacted using a co-culture system allowing or not direct contact between the cells.
  • the test compound is radiation, cells in culture medium may be submitted to radiation.
  • the test compound is a nucleic acid construct, it may be added to the culture medium in a suitable vehicle such as liposome, transfected or directly injected into the cells. All these techniques are well known by the skilled person.
  • step b) of the method the values of several mitochondrial behavior variables are measured in cells contacted with the test compound in step a). As shown in the experimental section, these variables have been selected by the inventors to constitute a HD-signature that is sufficient to segregate cells from HD patients to cells from healthy patients and that can be reversed when cells are contacted with a test compound useful in the treatment or prevention of HD.
  • the values of mitochondrial behavior variables are measured by analyzing images of mitochondria, preferably labeled mitochondria, observed in living cells. Images were taken, for example, at least every 10 s at high scan speed for at least 2 min, preferably every 0.1 to 10 s at high scan speed for at least 2 to 6 min.
  • the image capture may be carried out using any suitable microscopic technique such as fluorescent microscope or differential interference-contrast (DIC) microscope, coupled to an image acquisition system.
  • DIC differential interference-contrast
  • the image capture may be carried out using a fluorescent microscope.
  • mitochondria are not labeled
  • the image capture may be carried out using a DIC microscope.
  • the image acquisition device may be any device allowing capture of high-resolution frames at high speed such as a
  • the image capture is performed in three spatial dimensions.
  • the image capture may be thus carried out using a microscope equipped with a motorized plate allowing the visualization of a sample in three dimensions.
  • the measurements may be conducted in presence or after exposition to the test compound, preferably in presence of the test compound.
  • cells are kept at 37° C. during the image capture.
  • Mitochondria are mobile within the cell cytoplasm as they move along the cell microtubule and actin filament network and the first variable is selected from the group consisting of V1 and V34, and a combination thereof, wherein V1 is the average frequency of stops during trajectories of individual mitochondria and V34 is the average frequency of burst during displacement of individual mitochondria.
  • the variable V1 is the average frequency of stops during trajectories of individual mitochondria. This frequency is assessed by tracking each mitochondrion from frame to frame and recording the number of stops, i.e. the number of periods during which the mitochondrion remains immobile between two frames. The variable V1 is thus obtained by measuring the number of stops per unit time for each traced mitochondrion and calculating the average frequency of stops from data of all traced mitochondria.
  • the variable V34 is the average frequency of burst during displacement of individual mitochondria. This frequency is assessed by tracking each mitochondrion from frame to frame and recording the number of burst, i.e. the number of sudden displacements within 30% of the maximal displacements of the mitochondrion during the period of capture. The variable V34 is thus obtained by measuring the number of burst per unit time for each traced mitochondrion and calculating the average frequency of burst from data of all traced mitochondria.
  • the second variable, V12 is the average number of individual mitochondria per unit of cell area, or a dispersion descriptor of the numbers of individual mitochondria per unit of cell area. This number is preferably determined using an image analysis software by counting each mitochondrion on an image of the cell and expressing the result in number per unit of cell area, preferably per ⁇ m 2 of cell area.
  • the variable may be obtained by calculating the average number, of mitochondria per unit of cell from several measurements. This variable may also be obtained by calculating a dispersion descriptor, preferably selected from the group consisting of the variance, the standard deviation and an interquantile range, more preferably selected from the group consisting of the variance, the standard deviation and the interquartile range.
  • the third variable, V13 is the average area of mitochondria, or a dispersion descriptor of the areas of mitochondria.
  • the variable may be obtained by determining the area of each mitochondrion and calculating the average area from data of all observed mitochondria.
  • the variable may also be obtained by determining the area of each mitochondrion and calculating a dispersion descriptor of the areas of mitochondria.
  • the descriptor selected from the group consisting of the variance, the standard deviation and an interquantile range, more preferably selected from the group consisting of the variance, the standard deviation and the interquartile range.
  • the area of each mitochondrion is determined using an image analysis software.
  • the fourth variable, V15 is the frequency of mitochondria displaying an area between 0.51 and 1 ⁇ m 2 .
  • the 5 th variable, V23 is the frequency of mitochondria displaying an area between 10 and 20 ⁇ m 2 .
  • the 6 th variable is selected from the group consisting of V29, V7 and V30, and any combination thereof, wherein V29 is the frequency of mitochondria displaying an area between 70 and 100 ⁇ m 2 , V7 is the total area of regions containing entwined mitochondria to the total cell area, and V30 is the frequency of mitochondria displaying an area between 100 and 200 ⁇ m 2 .
  • the variables V15, V23, V29 and V30 relate to the frequency of mitochondria displaying a specific range of area.
  • the area of each mitochondrion is determined using image analysis software.
  • the variables V15, V23, V29 and V30 are thus obtained by measuring the area of mitochondria and determining the number of mitochondria displaying an area between 0.51 and 1 ⁇ m 2 , 10 and 20 ⁇ m 2 , 70 and 100 ⁇ m 2 and 100 and 200 ⁇ m 2 , respectively. The results are then expressed in percent of the total number of mitochondria.
  • variable V7 is the total area of regions containing tangled mitochondria, i.e. mitochondria that are interlaced to a point where individualisation of single mitochondria is impossible, to the total cell area. This variable assesses the concordance between the directionality of mitochondria with that of the cytoskeleton and is correlated to the state of the relationship between mitochondria and the cytoskeleton.
  • the 7 th variable is selected from the group consisting of V32 and V33, and a combination thereof, wherein V32 is the average moving speed of mitochondria, or a dispersion descriptor of moving speeds of mitochondria, and V33 is the average maximal moving speed of individual mitochondria, or a dispersion descriptor of maximal moving speeds of mitochondria.
  • the variable V32 is the average moving speed of mitochondria.
  • the moving speed of mitochondria is assessed by tracking each mitochondrion from frame to frame and recording the average speed of each mitochondrion.
  • the variable V32 may be then obtained by calculating the average moving speed of mitochondria from data of all traced mitochondria.
  • the variable may also be obtained by calculating a dispersion descriptor of the moving speeds of mitochondria.
  • the descriptor selected from the group consisting of the variance, the standard deviation and an interquantile range, more preferably selected from the group consisting of the variance, the standard deviation and the interquartile range.
  • the variable V33 is the average maximal moving speed of individual mitochondria.
  • the maximal speed is assessed by tracking each mitochondrion from frame to frame and recording the maximal speed of the mitochondrion reached during the capture.
  • the variable V33 may be then obtained by calculating the average maximal moving speed of mitochondria from data of all traced mitochondria.
  • the variable may also be obtained by calculating a dispersion descriptor of the maximal moving speeds of mitochondria.
  • the descriptor selected from the group consisting of the variance, the standard deviation and an interquantile range, more preferably selected from the group consisting of the variance, the standard deviation and the interquartile range.
  • a recording and data management device e.g. a computer with a suitable software, is used to record and analyze images of mitochondria observed through the microscope.
  • the number of mitochondria and cells to be analyzed for each variable is easily determined by the skilled person using statistic methods.
  • at least 50, 80 or 100 mitochondria are analyzed for each variable, preferably from at least 3, 10 or 15 cells.
  • at least 50, 80 or 100 mitochondria are analyzed for variables V1 and V32 and at least 100, 250, 500, 800, 900 or 1000 mitochondria are analyzed for variables V12, V13, V15, V23 and V29.
  • the method may comprise measuring the values of a combination of variables selected from the group consisting of V1, V12, V13, V15, V23, V29 and V32; V1, V12, V13, V15, V23, V7 and V32; V1, V12, V13, V15, V23, V7 and V33; V1, V12, V13, V15, V23, V30 and V32; V1, V12, V13, V15, V23, V30 and V32; V1, V12, V13, V15, V23, V30 and V33; V34, V12, V13, V15, V23, V29 and V32; V34, V12, V13, V15, V23, V29 and V33; V34, V12, V13, V15, V23, V29 and V33; V34, V12, V13, V15, V23, V7 and V32; V34, V12, V13, V15, V23, V7 and V32; V34, V12, V13,
  • the method comprises measuring the variables V1, V12, V13, V15, V23, V29 and V32 as defined above.
  • the method may further comprise measuring at least one additional variable selected from the group consisting of V7, V30 V33 and V34, as defined above.
  • the variables can be measured on samples from a population of HD patients. The values obtained for each variable are then averaged.
  • Each variable may be weighted in order to adjust their importance.
  • the method of screening of the invention may further comprise comparing the values of the variables obtained in step b) in presence of the test compound with the values obtained in absence of the test compound.
  • the values in absence of the test compound are obtained on cells from the same sample than in step b) before contacting the test compound.
  • these values are obtained after labelling mitochondria and before step a), i.e. on cells with labelled mitochondria before contacting the test compound.
  • the value of each variable is measured as detailed above. Values obtained without the test compound may be used as negative control to identify compounds that could be useful in the treatment of HD.
  • the method may also further comprise comparing the values of variables obtained in presence, and optionally in absence of the test compound, with the values of said variables measured in a sample obtained from a healthy subject (in absence of the test compound).
  • the healthy subject is about the same age as the HD patient providing the HD sample.
  • the value of each variable is measured as detailed above. Values obtained from the sample from the healthy subject may be used as positive control to identify compounds that could be useful in the treatment of HD. Alternatively, this positive control can be obtained by measuring the variables on samples from a population of healthy subject. The values obtained for each variable are then averaged.
  • the values of variables of the HD signature are measured in presence of several concentrations of the test compound in order to determine the dose-response effect of the test compound on HD.
  • the significance of differences of measured values may be determined using any suitable statistic test such as ANOVA.
  • the values obtained for the variables for each dose of the test compound may be represented as a score.
  • the effect of each dose may be evaluated in respect to the score obtained for the negative and/or positive controls.
  • the score for each variable may be calculated using the following ratio:
  • a global percentage of phenotypic rescue may be obtained by adding up the scores of each measured variable.
  • results may thus be expressed as a percentage of phenotypic rescue, the positive control (healthy sample) being 100% and the negative control (HD sample in absence of the test compound) being 0%.
  • Test compound providing a positive phenotypic rescue i.e. a compound that is able to partially or totally reverse the HD signature, is identified as potentially useful in the treatment of HD.
  • a test compound is identified as potentially useful if the phenotypic rescue is above 50%, more preferably above 60%, 70%, 80% or 90%.
  • a test compound is identified as potentially useful in the treatment of HD if all measured variables have a positive score, i.e. if a rescue is observed for each variable.
  • the present invention concerns a method for diagnosing Huntington disease in a subject, wherein the method comprises measuring in living cells obtained from a sample from said subject, the values of the mitochondrial behaviour variables (i) to (vii):
  • V1 the average frequency of stops during trajectories of individual mitochondria
  • V34 the average frequency of burst during displacement of individual mitochondria, and a combination thereof
  • V12 the average number of individual mitochondria per unit of cell area, or a dispersion descriptor of the numbers of individual mitochondria per unit of cell area;
  • V13 the average area of mitochondria, or a dispersion descriptor of the areas of mitochondria
  • V15 the frequency of mitochondria displaying an area between 0.51 and 1 ⁇ m 2 ;
  • V29 the frequency of mitochondria displaying an area between 70 and 100 ⁇ m 2
  • V7 the total area of regions containing entwined mitochondria to the total cell area
  • V30 the frequency of mitochondria displaying an area between 100 and 200 ⁇ m 2 , and any combination thereof
  • V32 the average moving speed of mitochondria, or a dispersion descriptor of the moving speeds of mitochondria
  • V33 the average maximal moving speed of individual mitochondria, or a dispersion descriptor of the maximal moving speeds of mitochondria, and a combination thereof.
  • the method may further comprise providing a sample from the subject.
  • mitochondria contained in living cells are labelled before measuring mitochondrial behavior variables.
  • the subject may have clinical signs that resemble HD or may be without any symptom.
  • the method may further comprise conducting a genetic test to determine the number of CAG repeats in the htt gene.
  • the subject comprises 36 to 39 CAG repeats in the htt gene.
  • the method of the invention is particularly relevant due to the impossibility to predict the penetrance of the disease from the number of CAG repeats.
  • the method may further comprise determining if said subject is affected with Huntington disease based on the measured values of mitochondrial behaviour variables.
  • the diagnosis of HD may be obtained by comparing the score obtained with the sample of the subject with the score of the sample obtained from a healthy patient or from a HD patient, or alternatively obtained from a population of healthy subjects or HD patients.
  • the method comprises measuring the mitochondrial behaviour variables V1, V12, V13, V15, V23, V29 and V32 as defined above, a gain of function in variables V1, V12 and V15 and a loss of function in variables V13, V23, V29 and V32, by comparison with the values of these variables obtained from a healthy sample, is indicative of HD.
  • the method may further comprise calculating the z-scores of measured variables. In particular, in HD sample the z-scores of variables V1, V12 and V15 are positive and the z-scores of variables V13, V23, V29 and V32 are negative.
  • the method comprises measuring the mitochondrial behaviour variables V1, V23 and V32 as defined above, a gain of function in variables V1 and V23 and a loss of function in variable V32, by comparison with the values of these variables obtained from a healthy sample, is indicative of HD.
  • the method may further comprise calculating the z-scores of measured variables. In particular, in HD sample the z-scores of variables V1, V23 and V32 are positive and the z-scores of variable V32 is negative.
  • the method may further comprise measuring the mitochondrial behaviour variables V13, V12, V15 and/or V29.
  • the present invention also concerns a method for providing useful information for the diagnosis of Huntington disease in a subject, wherein the method comprises measuring in living cells obtained from a sample from said subject the values of the mitochondrial behaviour variables (i) to (vii):
  • V1 the average frequency of stops during trajectories of individual mitochondria
  • V34 the average frequency of burst during displacement of individual mitochondria, and a combination thereof
  • V12 the average number of individual mitochondria per unit of cell area, or a dispersion descriptor of the numbers of individual mitochondria per unit of cell area;
  • V13 the average area of mitochondria, or a dispersion descriptor of the areas of mitochondria
  • V15 the frequency of mitochondria displaying an area between 0.51 and 1 ⁇ m 2 ;
  • V29 the frequency of mitochondria displaying an area between 70 and 100 ⁇ m 2
  • V7 the total area of regions containing entwined mitochondria to the total cell area
  • V30 the frequency of mitochondria displaying an area between 100 and 200 ⁇ m 2 , and any combination thereof
  • V32 the average moving speed of mitochondria, or a dispersion descriptor of the moving speeds of mitochondria
  • V33 the average maximal moving speed of individual mitochondria, or a dispersion descriptor of the maximal moving speeds of mitochondria, and a combination thereof.
  • the present invention also concerns a method for monitoring the response of a subject affected with Huntington disease to therapy, or for selecting a subject affected with Huntington disease for therapy, wherein the method comprises
  • V1 the average frequency of stops during trajectories of individual mitochondria
  • V34 the average frequency of burst during displacement of individual mitochondria, and a combination thereof
  • V12 the average number of individual mitochondria per unit of cell area, or a dispersion descriptor of the numbers of individual mitochondria per unit of cell area;
  • V13 the average area of mitochondria, or a dispersion descriptor of the areas of mitochondria
  • V15 the frequency of mitochondria displaying an area between 0.51 and 1 ⁇ m 2 ;
  • V29 the frequency of mitochondria displaying an area between 70 and 100 ⁇ m 2
  • V7 the total area of regions containing entwined mitochondria to the total cell area
  • V30 the frequency of mitochondria displaying an area between 100 and 200 ⁇ m 2 , and any combination thereof
  • V32 the average moving speed of mitochondria, or a dispersion descriptor of the moving speeds of mitochondria
  • V33 the average maximal moving speed of individual mitochondria, or a dispersion descriptor of the maximal moving speeds of mitochondria, and a combination thereof
  • step b comparing the measured values obtained before and after the administration of the treatment in step a).
  • mitochondria contained in living cells are labelled before measuring mitochondrial behavior variables.
  • the method may further comprise providing a sample from the subject before and/or after the administration of the treatment, preferably before and after the treatment.
  • the therapy may comprise administering one or several chemical or biological compounds, as well as radiations, as defined above.
  • the values obtained for the mitochondrial behaviour variables before and after the administration of the treatment may be represented as a score.
  • the effect of the treatment may be thus evaluated by comparing the scores obtained before and after the treatment.
  • the scores may also be compared with the score obtained from a healthy sample or from a population of healthy samples.
  • the patient is responsive to the therapy or is susceptible to benefit from the therapy when all measured variables have a positive score. If one or several variables have negative scores, the therapy may worsen the symptoms of the disease and should be stopped or avoided.
  • results may also be expressed as a percentage of phenotypic rescue, the positive control (healthy sample) being 100% and the negative control (HD sample without any treatment, e.g. the HD sample obtained before the treatment) being 0%.
  • a positive phenotypic rescue is indicative that the HD patient is responsive to the therapy or is susceptible to benefit from the therapy.
  • a negative phenotypic rescue indicates that the therapy may worsen the symptoms of the disease and should be stopped or avoided.
  • Skin biopsies were collected from 12 human donors comprising six healthy subjects and six HD patients (Table 1). No other disease or co-morbidity was reported in the two groups.
  • the cohort was chosen to minimize possible confounding age and gender effects by selecting only female subjects and by limiting the age range within roughly a decade around 36 or 38 in healthy and diseased subjects, respectively.
  • This selection also minimized the heterogeneity in the healthy population.
  • HD patients the duration of clinical manifestations of the disease prior to biopsy differed from one to ten years.
  • the clinical manifestation profiles were available for 4 HD patients out of 6. Chorea was present in two patients at different level of severity. One patient had a hypokinesic variant of HD with dystonia and marked tremor. One was marginally dystonic and showed bradykinesia and hypomimia, and another had bradykinesia.
  • the size of the CAG repeat was available for 4 HD patients and ranged from 47 to 69 CAG repeats on the mutant allele. One patient is homozygote and severely affected.
  • Patient-derived fibroblasts were cultured in DMEM containing 15% fetal calf serum. Cells of the sample were expanded and found stable for at least 16-20 passages.
  • Fibroblasts were labelled with MitoTracker green, a cell-permeant mitochondrial dye not sensitive to mitochondrial membrane potential, for 30 minutes. Images were recorded from an epifluorescence microscope continuously for 6 minutes. Cells were kept at 37° C. for the duration of the image capture. For each experimental condition, 3 to 15 cells were recorded per well from three independent plates, i.e. up to 6000 individual mitochondria. The maximum duration for data acquisition was 30 minutes (i.e. five cells observed during 6 min). Images were captured with a Zeiss Axioplan II microscope along three dimensions in space and in time.
  • V1, V32, V12, V13, V15, V23 and V29 seven variables (V1, V32, V12, V13, V15, V23 and V29) were found to be sufficient to segregate healthy and HD samples with only one misclassification (ID 090407).
  • V1 average frequency of stops during trajectories of individual mitochondria
  • V12 average number of individual mitochondria per unit of cell area, or variance, standard deviation or interquartile range of the measured values
  • V13 average area of mitochondria or variance, standard deviation or interquartile range of the measured values
  • V15 frequency of mitochondria displaying an area between 0.51 and 1 ⁇ m 2 ;
  • V23 frequency of mitochondria displaying an area between 10 and 20 ⁇ m 2 ;
  • V29 frequency of mitochondria displaying an area between 70 and 100 ⁇ m 2 ;
  • V32 average moving speed of mitochondria, or variance, standard deviation or interquartile range of the measured values
  • the dendogram of the hierarchical cluster analysis applying the Ward's method and obtained with the seven variables is shown in FIG. 1 .
  • the cluster analysis shows two subgroups composed of the diseased patient (top group) in which subject 090407 is misplaced, and a group of healthy subjects (bottom group).
  • the robustness of the signature comprising the seven variables was confirmed by analyzing about 39,000 additional mitochondria from 215 cells in 9 independent experiments and repeated the hierarchical cluster analysis.
  • Resveratrol is a plant polyphenol found in grapes and red wine. Resveratrol is associated with beneficial effects on aging, metabolic disorders, inflammation and cancer. Despite poor bioavailability, resveratrol was shown to rescue mutant huntingtin polyglutamine toxicity in several in vitro and in vivo models mimicking HD (Parker et al., 2005; Maher et al., 2011; Ho et al., 2010). Resveratrol may exert its effects by targeting several key metabolic sensor/effector proteins, such as AMPK, SIRT1, and PGC-1 ⁇ (Pasinetti et al., 2011).
  • Cyclosporine A is an anti-inflammatory drug inhibiting calcineurin.
  • Calcineurin is a Ca 2+ - and calmodulin-dependent protein serine-threonine phosphatase that is thought to play an important role in the neuronal response to changes in the intracellular Ca 2+ concentration.
  • Altered mitochondrial membrane potential and aberrant Ca 2+ handling are molecular mechanisms associated with HD and are targets of CSA (Choo et al., 2004).
  • CSA and FK506, another calcineurin inhibitor have been shown to have controversial effects on different animal models mimicking HD (Pineda et al., 2009; Kumar et al., 2010; Hernandez-Espinosa et al., 2006).
  • Patient-derived fibroblasts were cultured in DMEM containing 15% fetal calf serum. and 0.5% DMSO, a concentration known to be inert on the mitochondrial behaviour.
  • Resveratrol and CSA were tested at 4 doses spanning 3.5 log (10, 1, 0.1 and 0.05 ⁇ M).
  • the negative control was cells from HD patient (ID 090401) with the vehicle only and the positive control was cells from healthy patient (ID 071201) with the vehicle only.
  • Dose-response analysis of the effect of Resveratrol on the 7 variables constituting the HD-signature is shown in FIG. 4 . Effects are expressed as a percent of control values as defined above, i.e. % of phenotypic rescue. 0% represents the diseased status while 100% represents the healthy status.
  • the resulting activity profile ( FIG. 5 ) shows that 0.05 ⁇ M resveratrol provides a detrimental effect with a mild worsening of the diseased status while 0.1 and 1 ⁇ M provide 86 and 89.9% recovery, respectively. At 10 ⁇ M, the effect exceeds the healthy status. and may indicate over compensation.
  • Resveratrol thus shows disease-modifying capabilities and rescue of the disease status except at low dose.
  • Dose-response analysis of the effect of CSA on the 7 variables constituting the HD-signature is shown in FIG. 6 . Effects are expressed as a percent of control values as defined above, i.e. % of phenotypic rescue. 0% represents the diseased status while 100% represents the healthy status.
  • FIG. 7 shows dose-dependent loss of efficacy in the overall rescue of the diseased phenotype treated with CSA. Worsening of the beneficial effects of CSA at high dose (10 ⁇ M) may reflect its toxicity potential.
  • this signature can also be used as a surrogate marker for treatment efficacy, in particular in clinical trials.

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